/*
 * Licensed to the Apache Software Foundation (ASF) under one or more
 * contributor license agreements.  See the NOTICE file distributed with
 * this work for additional information regarding copyright ownership.
 * The ASF licenses this file to You under the Apache License, Version 2.0
 * (the "License"); you may not use this file except in compliance with
 * the License.  You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package org.apache.tika.parser.isatab;

import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.util.Collections;
import java.util.Set;

import org.xml.sax.ContentHandler;
import org.xml.sax.SAXException;

import org.apache.tika.config.TikaComponent;
import org.apache.tika.exception.TikaException;
import org.apache.tika.io.TemporaryResources;
import org.apache.tika.io.TikaInputStream;
import org.apache.tika.metadata.Metadata;
import org.apache.tika.mime.MediaType;
import org.apache.tika.parser.ParseContext;
import org.apache.tika.parser.Parser;
import org.apache.tika.sax.XHTMLContentHandler;

@TikaComponent
public class ISArchiveParser implements Parser {

    /**
     * Serial version UID
     */
    private static final long serialVersionUID = 3640809327541300229L;
    private static String studyAssayFileNameField = "Study Assay File Name";
    private final Set<MediaType> SUPPORTED_TYPES =
            Collections.singleton(MediaType.application("x-isatab"));
    private String location = null;

    private String studyFileName = null;

    /**
     * Default constructor.
     */
    public ISArchiveParser() {
        this(null);
    }

    /**
     * Constructor that accepts the pathname of ISArchive folder.
     *
     * @param location pathname of ISArchive folder including ISA-Tab files
     */
    public ISArchiveParser(String location) {
        if (location != null && !location.endsWith(File.separator)) {
            location += File.separator;
        }
        this.location = location;
    }

    @Override
    public Set<MediaType> getSupportedTypes(ParseContext context) {
        return SUPPORTED_TYPES;
    }

    @Override
    public void parse(InputStream stream, ContentHandler handler, Metadata metadata,
                      ParseContext context) throws IOException, SAXException, TikaException {

        TemporaryResources tmp =
                TikaInputStream.isTikaInputStream(stream) ? null : new TemporaryResources();

        TikaInputStream tis = TikaInputStream.get(stream, tmp, metadata);
        try {
            if (this.location == null) {
                this.location = tis.getFile().getParent() + File.separator;
            }
            this.studyFileName = tis.getFile().getName();

            File locationFile = new File(location);
            String[] investigationList = locationFile.list((dir, name) -> name.matches("i_.+\\.txt"));

            XHTMLContentHandler xhtml = new XHTMLContentHandler(handler, metadata);
            xhtml.startDocument();

            parseInvestigation(investigationList, xhtml, metadata, context);
            parseStudy(stream, xhtml, metadata, context);
            parseAssay(xhtml, metadata, context);

            xhtml.endDocument();
        } finally {
            if (tmp != null) {
                tmp.dispose();
            }
        }
    }

    private void parseInvestigation(String[] investigationList, XHTMLContentHandler xhtml,
                                    Metadata metadata, ParseContext context)
            throws IOException, SAXException, TikaException {
        if ((investigationList == null) || (investigationList.length == 0)) {
            // TODO warning
            return;
        }
        if (investigationList.length > 1) {
            // TODO warning
            return;
        }

        String investigation = investigationList[0]; // TODO add to metadata?
        try (InputStream stream = TikaInputStream.get(new File(this.location + investigation).toPath())) {
            ISATabUtils.parseInvestigation(stream, xhtml, metadata, context, this.studyFileName);
        }
        xhtml.element("h1", "INVESTIGATION " + metadata.get("Investigation Identifier"));
    }

    private void parseStudy(InputStream stream, XHTMLContentHandler xhtml, Metadata metadata,
                            ParseContext context) throws IOException, SAXException, TikaException {
        xhtml.element("h2", "STUDY " + metadata.get("Study Identifier"));

        ISATabUtils.parseStudy(stream, xhtml, metadata, context);
    }

    private void parseAssay(XHTMLContentHandler xhtml, Metadata metadata, ParseContext context)
            throws IOException, SAXException, TikaException {
        for (String assayFileName : metadata.getValues(studyAssayFileNameField)) {
            xhtml.startElement("div");
            xhtml.element("h3", "ASSAY " + assayFileName);
            // location starts with "/C:" on windows, can't use Paths.get()
            try (InputStream stream = TikaInputStream.get(new File(this.location + assayFileName).toPath()))
            {
                ISATabUtils.parseAssay(stream, xhtml, metadata, context);
            }
            xhtml.endElement("div");
        }
    }
}
